Molecular characterization of grapevine rupestris stem pitting-associated virus isolates infecting grapevines in Serbia

Abstract

Grapevine rupestris stem pitting-associated virus (GRSPaV) occurs worldwide and is often considered to be one of the most prevalent grapevine viruses. It is involved in the graft-transmissible disease rupestris stem pitting of the rugose wood complex, as well as in the vein necrosis and Syrah decline, although its role in all diseases is not yet clear. In addition, GRSPaV is also found in grapevine cultivars in a latent state. After the first detection, two-year survey (2021-2022) was carried out to determine the presence and distribution of the virus in Serbia and to examine its genetic diversity. A total of 55 samples were collected and analyzed by the multiplex reverse transcription-polymerase chain reaction (mRT-PCR) using primers for nine viruses that commonly infect grapevine: arabis mosaic virus (ArMV), grapevine fanleaf virus (GFV), grapevine virus A (GVA) and B (GVB), GRSPaV, grapevine fleck virus (GFkV), grapevine leafroll-associated virus-1 (GLRaV-1), -2 (GLRaV-2), and -3 (GLRaV-3). The presence of GRSPaV was detected in 66.6% of the samples tested in single or mixed infections with GVA, GLRaV-1, -3, GFkV and/or ArMV. For further GRSPaV molecular characterization, seven mRT-PCR positive isolates were selected and a fragment of the coat protein (CP) gene was partially sequenced. Multiple alignments of the sequences revealed nucleotide identities from 83.9% to 97.9%, indicating variability of the GRSPaV population in Serbia. Phylogenetic analysis revealed that genetic variability of GRSPaV comprising three molecular variants is present in Serbian grapevine genotypes. Although GRSPaV is considered a virus of minor importance, the virus may pose a risk for severe decline symptoms caused by either single or complex infections with other viruses. This study has also shown that the virus is highly prevalent in Serbia and that enhanced phytosanitary measures are needed to exclude GRSPaV in vines used for vineyard propagation and planting.